Changeset edb650 for src/builder.cpp

Timestamp:

Jun 13, 2008, 2:26:50 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

14d4d4

Parents:

318bfd

Message:

some mor changes to fine-tune the cluster generation.

Sadly, VolumeOfConvexEnvelope() is not robust/stable, with Ratio1.4-1/1800K/compundH.*.xyz no usable convex envelope was found but points were connected right through the cluster.

File:

• src/builder.cpp (modified) (3 diffs)

src/builder.cpp

@@ -736 +736 @@
   int ExitFlag = 0;
   int j;
+  double volume = 0.;
   enum ConfigStatus config_present = absent;
   clock_t start,end;
@@ -987 +988 @@
               VolumeOfConvexEnvelope((ofstream *)&cout, &configuration, NULL, mol);
               break;
+            case 'U':
+              volume = atof(argv[argptr++]);
+              cout << Verbose(0) << "Using " << volume << " angstrom^3 as the volume instead of convex envelope one's." << endl;  
             case 'u':
               {
-                double tmp;
+                double density;
                 ExitFlag = 1;
                 cout << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.";
-                tmp = atof(argv[argptr++]);
-                if (tmp < 1.0) {
+                density = atof(argv[argptr++]);
+                if (density < 1.0) {
                   cerr << Verbose(0) << "Density must be greater than 1.0g/cm^3 !" << endl;
-                  tmp = 1.3;
+                  density = 1.3;
                 }
 //                for(int i=0;i<NDIM;i++) {
@@ -1003 +1007 @@
 //                  repetition[i] = 1;
 //                }
-                PrepareClustersinWater((ofstream *)&cout, &configuration, mol, tmp);
+                PrepareClustersinWater((ofstream *)&cout, &configuration, mol, volume, density);
               }
               break;